Computational protocol: Association of KCTD10, MVK, and MMAB polymorphisms with dyslipidemia and coronary heart disease in Han Chinese population

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Protocol publication

[…] Based on the public HapMap SNP database (phase II + III Feb 09, on NCBI B36 assembly, dbSNP b126) and the HaploView 4.2 software, common SNPs (MAF ≥0.05) in the three genes (MVK, MMAB and KCTD10) were screened in gene regions (including 2-kb up-stream region of each gene) in Chinese Han population. A total of 21 potentially functional SNPs were selected after the prediction by using SNPinfo Web Server (http://snpinfo.niehs.nih.gov/) which is a comprehensive web-based tool designed to select SNPs based on GWAS results, linkage disequilibrium, and predict potential functional characteristics of polymorphisms. Besides, in order to validate the findings of GWAS [, ], rs2338104 and rs7134594 were also included. However, three SNPs were excluded for the failed probe design and two SNPs were removed due to genotyping failure (call rates <95 %). As a result, 18 loci were finally included in the current study. The linkage disequilibrium (LD) association for the 18 loci was further analyzed (Additional file : Figure S1). […]

Pipeline specifications

Software tools Haploview, SNPinfo
Databases dbSNP
Application GWAS
Diseases Coronary Disease, Dyslipidemias
Chemicals Cholesterol, Mevalonic Acid, Potassium